Alignment of HL_37344.1 sequences from 3D to the JAR3D model

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The correspondence between sequences from 3D structures and the motif group is shown in blue and the JAR3D alignment of the sequences to the motif group is shown in black. Occasionally the two disagree, in which case the JAR3D alignment is shown in red.
Column number:
Node in JAR3D model:
Insertion positions indicated by I:
Position in motif group:		1
1
I

2
2

1
3
2
I

4
3

2
5
3
I

6
4

3
7
4
I

8
4

4
9
3
I

10
3

5
11
2
I

12
2

6
13
1
I


In
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Alignment
score
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HL_37344.1_Instance_1 HL_37344.1,HL_8P9A_233,C2567_G2574CCAUUCGG
HL_37344.1_Sequence_1 HL_37344.18P9A_C_2567_G_2574CCAUUCGGtrue85001.62
HL_37344.1_Instance_2 HL_37344.1,HL_5J7L_018,C840_G846CCUUGAG
HL_37344.1_Sequence_2 HL_37344.15J7L_C840_G846CCUUGAGtrue100000.00

Conserved interactions between motif group positions in HL_37344.1:
1 2 s35 
1 6 cWW 
2 4 s35 
2 5 cWW 
2 6 s55 
3 4 perp 
4 5 s55 
5 6 s35
JAR3D SCFG/MRF model for HL_37344.1:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [6] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair C2567 - G2574 cWW 
BasepairNode | Deletion Probability [0.0000000083615247] | Pair Probability [[0.010352875,0.015863081,0.012591569,0.114801277,0.000000000],[0.199454072,0.025352662,0.131709272,0.014834628,0.000000000],[0.012824089,0.116226614,0.002839997,0.019325897,0.000000000],[0.120040710,0.013878720,0.177652981,0.012251556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.011890606,0.487514863,0.487514863,0.012485137,0.000594530] | Right Letter Distribution [0.100000000,0.300000000,0.300000000,0.300000000,0.000000000] | Left Index [2] | Right Index [5] // Basepair C2568 - G2573 cWW 
HairpinNode  | Num Bases [2] | Left Index [3] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A2569:U2570
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2569
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.625000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U2570
Sequences of instances from HL_37344.1:
> HL_37344.1  8P9A C 2567 G 2574
CCAUUCGG
> HL_37344.1  5J7L C  840 G  846
CCUUGAG